The entire structure for scientificating was built on a single assumption.
It's built on the idea that yes, we CAN use our senses and reason to understand the world around us and how it works, and use our knowledge to change it to suit ourselves. This idea has been proven correct.
This assumption was a modification to Aristotle's metaphysics which has its roots in Catholic friars such as Thomas and Scotus. In their efforts to adapt the pagan's system to the Bible, they invented new concepts such as being and essence. When Newton made his operational definition of time and space, he did so mathematically using the notion that the ESSENCE of substance is changeless.
And none of these people represent the last word in science, math or any other field. You seem incapable of understanding that yes, theories CAN and MUST change when observation does not match hypothesis, and that, rather than being a weakness, it is this that gives science its strength.
No one has ever detected any essence or being. In fact the visible properties of all matter are observed to continue to change throughout cosmic history.
If you are referring to supposed C-decay, no, that hasn't been observed. Tens of thousands of observations of distant objects have yet to discover any evidence that the speed of light has changed over time. The evidence that creationists try to use to support it were obtained by cherry-picking the data and ignoring experiments that did not agree with their theory.
There is an ongoing attempt in physics to determine if ANY physical constants have changed over time in the course of the universe's existence, or over the entire volume of the observable universe. There IS a small amount of data that suggests that the Fine-Structure Constant has changed very slightly over time, and that it may be very slightly different between halves of the universe observed between the northern and southern hemispheres--by about 1 part in 100,000. Research is ongoing, but even if this happens to be true, it won't have the effect you think it does, and there is little, if any, evidence that the dimensional physical constants such as G, c, h, or e0 have changed.
As far back as you care to go, matter and energy appear to have been behaving in much the same way as we seem them now. So no, wrong again.
Even local clocks that transmitted their precision signals yesterday do not match with clock that emit their clocks frequencies today (the Pioneers).
The Pioneer anomaly is most likely caused by the very small but constant acceleration caused by thermal radiation leaking from the spacecraft. The idea of it leading to new physics, while very exciting, is almost certainly wrong, if that's what you're referencing.
If you're talking about the fact that time moves at a different rate for the Pioneer spacecraft than it does here on Earth, congratulations--you've actually discovered Relativity, in pretty much exactly the same way that a blind man discovers a hole. Time DOES, in fact, move a different rate for them, as it does for the Voyagers, the Cassini spacecraft, the ISS, GPS satellites in orbit, and fast-moving aircraft. Time moves at a different rate if you're at different positions in a gravity well, if you're moving, or if you're moving in a different direction relative to something else. And we can mathematically calculate the difference, measure it, and see that our calculations agree with both our observations AND THEORIES because it is predictable, and because we have to be able to compensate for the difference from second to second in order to launch, and retain contact with, a spacraft, much less make it do anything useful, because it even affects how their computers and instruments work.
The horror of empiricism is that they define almost all of their measuring units in a double circle.
If by that, you're trying to say that we make theories based on what we observe and that we accept or reject that theory based on how closely it matches what we actually see you're right. You seem to regard this as a Very Bad Thing. I suspect you're getting at some form of Plato's Cave Hypothesis, and that the only way you can see out of it is by some form of revealed, capital-T Truth handed down from on high.
They actually believe that mass, energy and time exist even though they are utterly undetectable and can only be measured mathematically with other undetectable things circularly.
They're not undetectable unless you've chosen to reject all evidence from your senses as false or misleading, and we know they exist because it actually works, it actually can be used to create or do something we find useful.
Almost all of them were contrived using the assumption Peter predicted for the false teachers of the last days.
Then stop using your computer, stop watching television or listening to a radio, and retreat to the desert somewhere where you can raise your food and live in a hut waiting for the end, since virtually everything around you that you use on a daily basis was created with the science, chemistry, and physics you don't trust.